PMEMD is on a timer, such that it actually only updates mdinfo at some
interval (I am thinking once per minute or some such); I absolutely would
not dink with that feature, as writing mdinfo actually does increase i/o
loading. Just adding the stuff here probably won't matter that much though.
- Bob
----- Original Message -----
From: "Ross Walker" <ross.rosswalker.co.uk>
To: "'AMBER Developers Mailing List'" <amber-developers.ambermd.org>
Sent: Saturday, December 19, 2009 7:43 PM
Subject: [AMBER-Developers] Updated mdinfo file.
> Hi All,
>
> I have made some updates to the information that is printed to the mdinfo
> file to try to make it a little more useful. Sander now prints information
> about performance and estimated runtime remaining to the mdinfo file
> everytime ntpr is triggered. This should help when running in queues for
> example with limited wallclock runtime where one can see very quickly if a
> job is expected to finish in time. The output looks as follows:
>
>> cat mdinfo
>
> NSTEP = 300 TIME(PS) = 510.350 TEMP(K) = 297.90 PRESS =
> 0.0
> Etot = -57751.9944 EKtot = 13952.0308 EPtot =
> -71704.0252
> BOND = 450.7895 ANGLE = 1266.9584 DIHED =
> 972.3826
> 1-4 NB = 542.4150 1-4 EEL = 6650.2876 VDWAALS =
> 8097.2637
> EELEC = -89684.1221 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.9893E-04
>
> ----------------------------------------------------------------------------
> --
> | Current Timing Info
> | -------------------
> | Total steps : 20000 | Completed : 300 | Remaining : 19700
> |
> | Average timings for last 50 steps:
> | Elapsed(s) = 2.2 Per Step(ms) = 43.9
> | ns/day = 2.0 seconds/ns = 43881.0
> |
> | Average timings for all steps:
> | Elapsed(s) = 13.0 Per Step(ms) = 43.4
> | ns/day = 2.0 seconds/ns = 43354.8
> |
> | Estimated time remaining: 14.2 minutes.
>
> ----------------------------------------------------------------------------
> --
>
> I will update PMEMD to print the same info shortly.
>
> Comments?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
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>
>
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Received on Sat Dec 19 2009 - 17:30:02 PST
